Polygenic Score (PGS) ID: PGS004879

Predicted Trait
Reported Trait Coronary heart disease
Mapped Trait(s) coronary artery disease (EFO_0001645)
Released in PGS Catalog: June 27, 2024
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name INTERVENE_MegaPRS_CHD
Development Method
Name megaprs.auto
Parameters BayesR, p1=0.89, p2=0.05, p3= 0.05, p4=0.01
Variants
Original Genome Build GRCh37
Number of Variants 610,677
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000618
Citation (link to publication) Jermy B et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • Not Reported
63,731 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
7 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004787
Europe PMC: 28714975
 63,731 individuals European, NR NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 404 individuals European 1000G — — — non-Finnish Europeans —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM021209 PSS011573|
European Ancestry|
38,448 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident CHD HR: 1.18 [1.16, 1.2] C-index: 0.55 [0.55, 0.56] — PCs 1-10 —
PPM021210 PSS011572|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident CHD HR: 1.39 [1.36, 1.42] C-index: 0.6 [0.59, 0.6] — PCs 1-10 —
PPM021211 PSS011571|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident CHD HR: 1.32 [1.27, 1.38] C-index: 0.6 [0.58, 0.61] — PCs 1-10 —
PPM021212 PSS011569|
European Ancestry|
44,168 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident CHD HR: 1.27 [1.23, 1.32] — — PCs 1-10 —
PPM021213 PSS011570|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident CHD HR: 1.13 [1.07, 1.19] C-index: 0.56 [0.54, 0.57] — PCs 1-10 —
PPM021214 PSS011568|
European Ancestry|
412,090 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident CHD HR: 1.41 [1.4, 1.43] C-index: 0.62 [0.62, 0.62] — PCs 1-10 —
PPM021215 PSS011567|
European Ancestry|
148,312 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident CHD HR: 1.18 [1.16, 1.21] C-index: 0.58 [0.57, 0.58] — PCs 1-10 —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS011567 — —
[
  • 8,099 cases
  • , 140,213 controls
]
 — European — EB —
PSS011568 — —
[
  • 41,144 cases
  • , 370,946 controls
]
 — European — FinnGen —
PSS011569 — —
[
  • 3,014 cases
  • , 41,154 controls
]
 — European — G&H —
PSS011570 — —
[
  • 1,260 cases
  • , 5,758 controls
]
 — European — GS:SFHS —
PSS011571 — —
[
  • 2,267 cases
  • , 27,160 controls
]
 — European — GEL —
PSS011572 — —
[
  • 9,039 cases
  • , 60,676 controls
]
 — European — HUNT —
PSS011573 — —
[
  • 11,491 cases
  • , 26,957 controls
]
 — European — MGBB —